Coexpression cluster:C4572: Difference between revisions

Revision as of 16:49, 26 November 2012

Full id: C4572_breast_lung_choriocarcinoma_thyroid_immature_throat_amniotic

Phase1 CAGE Peaks

Hg19::chr6:144651917..144651928,+	p@chr6:144651917..144651928 +
Hg19::chr6:144651933..144651949,+	p@chr6:144651933..144651949 +
Hg19::chr6:144651950..144651997,+	p@chr6:144651950..144651997 +

Enriched pathways on this co-expression clusterSummary: Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons. Analyst: Emmanuel Dimont link to source dataset data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. Analyst: Erik Arner link to source dataset data

No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary:To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. Analyst: Hideya Kawaji links to source dataset cell_data uberon_data disease_data

Cell Type
Ontology term	p-value	n
endo-epithelial cell	5.61e-16	42
endodermal cell	6.46e-12	58
epithelial cell of alimentary canal	4.31e-09	20

Uber Anatomy
Ontology term	p-value	n
endoderm-derived structure	5.04e-14	160
endoderm	5.04e-14	160
presumptive endoderm	5.04e-14	160
digestive system	1.03e-13	145
digestive tract	1.03e-13	145
primitive gut	1.03e-13	145
respiratory system	5.90e-12	74
subdivision of digestive tract	4.86e-11	118
adult organism	1.32e-09	114
epithelial bud	4.76e-09	37
respiratory tract	8.60e-09	54
anatomical space	1.81e-08	95
orifice	2.16e-08	36
endo-epithelium	2.32e-08	82
organ system subdivision	7.49e-08	223
organ	8.96e-08	503
foregut	1.57e-07	87
oral opening	3.47e-07	22
immaterial anatomical entity	5.53e-07	117
thoracic cavity element	5.58e-07	34
thoracic cavity	5.58e-07	34
epithelial fold	5.72e-07	47
reproductive structure	6.10e-07	59
reproductive system	6.10e-07	59
male organism	7.21e-07	22
male reproductive system	7.21e-07	22

Disease
Ontology term	p-value	n
carcinoma	5.31e-10	106
adenocarcinoma	3.99e-09	25
cell type cancer	9.48e-07	143

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary:The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. Analyst: Michiel de Hoon link to source data Novel motifs data Jaspar motifs data

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysisSummary: For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. Analyst: Erik Arner link to source dataset data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
BCL11A#53335	3	28.3694551036071	4.37778126761649e-05	0.000779691503766368
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168269950190494
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00583729699062021
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.00085444298567922
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157556058662846
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295832284759843
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000740538397129569
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00309999931872347
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247689133943701
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109367577853583
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00545232864621491
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00631688710085641
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330999494816262

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. Analyst:NA link to data source data

This analysis result is provided for C0 - C305 clusters.

@@ Line 8: / Line 8: @@
 |tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000779691503766368!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168269950190494!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583729699062021!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.00085444298567922!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157556058662846!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295832284759843!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000740538397129569!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309999931872347!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247689133943701!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109367577853583!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00545232864621491!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631688710085641!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330999494816262
 |tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.000938367,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.324808,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.0400492,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.0216297,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.00708381,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.00411171,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.0134864,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.0163125,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.355018,0.782949,0.635872,0.051522,0.823736,0.489965,0.335423,0.629514,0.261553,0.446302,0.373681,0.053682,0.49143,0.330703,0.395854,0.329568,0.53472,0.615744,0.271958,0.292154,0.405773,0.39729,0.217139,0.0139202,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.056723,0.608919,0.18237,0.706298,0.821217,0.161148,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.155555,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.581837,0.412837,0.305671,0.546839,0.551561,0.448039,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.229003,0.650179,0.589326,0.50215,0.0054714,0.0671437,0.477304,0.289204,0.327108,0.683186,0.278044,0.807485,0.428671,0.0282539,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.420626,0.516462,0.858756,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.00696513,0.284629,0.262537,0.010587,0.226257,0.405955,0.41707,0.0760312,0.130283,0.753577,0.206222,0.525396,0.651524,0.437176,0.040018,0.339277,0.552319,0.00470507,0.141758,0.455379,0.168058,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.0158269,0.0847452,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.000397518,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.0135691,0.123526,0.0906475,0.0558058,0.28262,0.5177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1435
+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,1.11965,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,0.151453,0.726632,0.939121,0.808003,2.77373,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,2.87582,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,2.40384,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,1.98143,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,0.0768232
 }}

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Coexpression cluster:C4572: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:49, 26 November 2012

Phase1 CAGE Peaks

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